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- PDB-4hkq: XMRV reverse transcriptase in complex with RNA/DNA hybrid -

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Basic information

Entry
Database: PDB / ID: 4hkq
TitleXMRV reverse transcriptase in complex with RNA/DNA hybrid
Components
  • DNA (5'-D(*TP*GP*GP*AP*AP*TP*CP*A*GP*GP*TP*GP*TP*CP*GP*CP*AP*CP*TP*CP*TP*G)-3')
  • RNA (5'-R(*AP*AP*CP*AP*GP*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*CP*AP*U)-3')
  • Reverse transcriptase/ribonuclease H p80
KeywordsTRANSCRIPTION/RNA/DNA / Protein-DNA-RNA complex / reverse transcription / TRANSCRIPTION-RNA-DNA complex
Function / homology
Function and homology information


virion assembly / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity ...virion assembly / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / ribonuclease H / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / structural constituent of virion / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / host cell plasma membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane / identical protein binding
Similarity search - Function
Ubiquitin-like (UB roll) - #370 / Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 ...Ubiquitin-like (UB roll) - #370 / Gag-Pol polyprotein, Zinc-finger like domain / Murine leukemia virus integrase, C-terminal / Zinc-finger like, probable DNA-binding / Murine leukemia virus (MLV) integrase (IN) C-terminal domain / Gamma-retroviral matrix protein / Gag polyprotein, inner coat protein p12 / Core shell protein Gag P30 / Matrix protein (MA), p15 / Gag polyprotein, inner coat protein p12 / Gag P30 core shell protein / Gamma-retroviral matrix domain superfamily / Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain / RNase H-like domain found in reverse transcriptase / HIV Type 1 Reverse Transcriptase, subunit A, domain 1 / HIV Type 1 Reverse Transcriptase; Chain A, domain 1 / Reverse transcriptase/Diguanylate cyclase domain / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Ubiquitin-like (UB roll) / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / Roll / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA / RNA (> 10) / Gag-Pol polyprotein
Similarity search - Component
Biological speciesXenotropic MuLV-related virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.04 Å
AuthorsNowak, E. / Potrzebowski, W. / Konarev, P.V. / Rausch, J.W. / Bona, M.K. / Svergun, D.I. / Bujnicki, J.M. / Le Grice, S.F.J. / Nowotny, M.
CitationJournal: Nucleic Acids Res. / Year: 2013
Title: Structural analysis of monomeric retroviral reverse transcriptase in complex with an RNA/DNA hybrid
Authors: Nowak, E. / Potrzebowski, W. / Konarev, P.V. / Rausch, J.W. / Bona, M.K. / Svergun, D.I. / Bujnicki, J.M. / Le Grice, S.F. / Nowotny, M.
History
DepositionOct 15, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references / Structure summary
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reverse transcriptase/ribonuclease H p80
E: RNA (5'-R(*AP*AP*CP*AP*GP*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*CP*AP*U)-3')
F: DNA (5'-D(*TP*GP*GP*AP*AP*TP*CP*A*GP*GP*TP*GP*TP*CP*GP*CP*AP*CP*TP*CP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)90,9683
Polymers90,9683
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-23 kcal/mol
Surface area23710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.132, 98.132, 201.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Reverse transcriptase/ribonuclease H p80 / RT


Mass: 76202.523 Da / Num. of mol.: 1 / Fragment: Reverse Transcriptase, UNP residues 658-1328 / Mutation: D583N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenotropic MuLV-related virus / Strain: VP62 / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) Magic
References: UniProt: A1Z651, RNA-directed DNA polymerase, DNA-directed DNA polymerase, ribonuclease H
#2: RNA chain RNA (5'-R(*AP*AP*CP*AP*GP*AP*GP*UP*GP*CP*GP*AP*CP*AP*CP*CP*UP*GP*AP*UP*UP*CP*CP*AP*U)-3')


Mass: 7981.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Random sequence for RNA
#3: DNA chain DNA (5'-D(*TP*GP*GP*AP*AP*TP*CP*A*GP*GP*TP*GP*TP*CP*GP*CP*AP*CP*TP*CP*TP*G)-3')


Mass: 6783.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Random sequence for DNA
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.94 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 17% PEG 3350, 0.1M Bis-Tris, 0.2M Ammonium Sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID23-210.872
SYNCHROTRONBESSY 14.120.979
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDNov 14, 2011
MARMOSAIC 225 mm CCD2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.8721
20.9791
ReflectionResolution: 3.04→50 Å / Num. all: 19791 / Num. obs: 19791 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 13 % / Biso Wilson estimate: 71.4 Å2
Reflection shellResolution: 3.04→3.09 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RW3

1rw3
PDB Unreleased entry


Resolution: 3.04→29.661 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7658 / SU ML: 0.39 / σ(F): 2 / Phase error: 28.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2798 981 5.12 %Random
Rwork0.2242 ---
all0.227 19791 --
obs0.227 19172 97.37 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.648 Å2 / ksol: 0.327 e/Å3
Displacement parametersBiso max: 198.25 Å2 / Biso mean: 78.1723 Å2 / Biso min: 29.51 Å2
Baniso -1Baniso -2Baniso -3
1-7.3011 Å20 Å2-0 Å2
2--7.3011 Å2-0 Å2
3----14.6021 Å2
Refinement stepCycle: LAST / Resolution: 3.04→29.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3413 621 0 37 4071
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114238
X-RAY DIFFRACTIONf_angle_d1.0115867
X-RAY DIFFRACTIONf_dihedral_angle_d16.2571616
X-RAY DIFFRACTIONf_chiral_restr0.06677
X-RAY DIFFRACTIONf_plane_restr0.005649
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.04-3.20010.42311330.3316235191
3.2001-3.40030.38291490.2747249695
3.4003-3.66250.30171300.2464255498
3.6625-4.03020.29691550.2178258699
4.0302-4.61150.24541420.17622646100
4.6115-5.80290.20321320.1922704100
5.8029-29.66270.27681400.2382854100

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